bioexcel / biobb_gromacs

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Solvate does not zip a custom .itp included in .top ¿at random? #22

Closed frannerin closed 3 months ago

frannerin commented 3 months ago

I am setting up systems to run RBFE calculations, so a protein+ligand system and a ligand-only system. In the ".top" files of both systems I include both 'ffMOL2.itp', with the atom types and vdW parameters of the ligand (incl. dummy atoms), and 'merged.itp', with merged parameters of the hybrid ligand.

However, when using the Solvate block, everything runs correctly but the output .zip file of the ligand-only system, with all the necessary files for the topology, does not include 'merged.itp', while for the protein+ligand system it is included in the .zip normally. Looking at the logs of the ligand-only solvate run, 'merged.itp' is correctly unzipped from the input .zip topology, but in the end to zip everything back it is not detected at all, not even as a file to ignore, like the ff or the water .itp. It looks like it is not detected at all by the relevant biobb_common.tools methods.

I include the input files and code (.ipynb) to reproduce.

bug.zip

Environment ``` $conda list # packages in environment at /home/francho.nerin-fonz/miniforge3/envs/biobb_wf_pmx_tutorial: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _sysroot_linux-64_curr_repodata_hack 4 h5bd9786_17 conda-forge ambertools 23.3 py310hc095264_3 conda-forge amberutils 21.0 pypi_0 pypi anyio 4.4.0 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge arpack 3.8.0 nompi_h0baa96a_101 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge binutils 2.40 h4852527_7 conda-forge binutils_impl_linux-64 2.40 ha1999f0_7 conda-forge binutils_linux-64 2.40 hb3c18ed_0 conda-forge biobb_analysis 4.2.0 pyhdfd78af_0 bioconda biobb_common 4.2.0 pyhdfd78af_0 bioconda biobb_gromacs 4.2.0 pyhdfd78af_0 bioconda biobb_pdb_tools 4.2.0 pyhdfd78af_0 bioconda biobb_pmx 4.2.1 pyhdfd78af_0 bioconda biopython 1.84 py310hc51659f_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc 1.21.6 hef167b5_0 conda-forge boost 1.78.0 py310hcb52e73_5 conda-forge boost-cpp 1.78.0 h2c5509c_4 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.32.3 h4bc722e_0 conda-forge c-compiler 1.7.0 hd590300_1 conda-forge ca-certificates 2024.7.4 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.18.0 hbb29018_2 conda-forge certifi 2024.7.4 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge chardet 5.2.0 py310hff52083_1 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py310hd41b1e2_0 conda-forge curl 8.9.0 h18eb788_0 conda-forge cxx-compiler 1.7.0 h00ab1b0_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.10 py310hc6cd4ac_0 conda-forge debugpy 1.8.2 py310h76e45a6_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge edgembar 0.2 pypi_0 pypi entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fftw 3.3.10 nompi_hf1063bd_110 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 py310h5b4e0ec_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge gcc 12.4.0 h236703b_0 conda-forge gcc_impl_linux-64 12.4.0 hb2e57f8_0 conda-forge gcc_linux-64 12.4.0 h6b7512a_0 conda-forge greenlet 3.0.3 py310hc6cd4ac_0 conda-forge gromacs 2022.2 nompi_hca75aac_100 conda-forge gxx 12.4.0 h236703b_0 conda-forge gxx_impl_linux-64 12.4.0 h557a472_0 conda-forge gxx_linux-64 12.4.0 h8489865_0 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 8.2.0 pyha770c72_0 conda-forge importlib-resources 6.4.0 pyhd8ed1ab_0 conda-forge importlib_metadata 8.2.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge ipykernel 6.29.5 pyh3099207_0 conda-forge ipython 8.18.1 pyh707e725_3 conda-forge ipywidgets 8.1.3 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge json5 0.9.25 pyhd8ed1ab_0 conda-forge jsonpointer 3.0.0 py310hff52083_0 conda-forge jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge jupyter 1.0.0 pyhd8ed1ab_10 conda-forge jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py310hff52083_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.2.4 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.11 pyhd8ed1ab_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libblas 3.9.0 23_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 23_linux64_openblas conda-forge libcurl 8.9.0 hdb1bdb2_0 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.4.0 ha4f9413_100 conda-forge libgcc-ng 14.1.0 h77fa898_0 conda-forge libgfortran-ng 14.1.0 h69a702a_0 conda-forge libgfortran5 14.1.0 hc5f4f2c_0 conda-forge libglib 2.80.3 h8a4344b_1 conda-forge libgomp 14.1.0 h77fa898_0 conda-forge libhwloc 2.8.0 h32351e8_1 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 23_linux64_openblas conda-forge libnetcdf 4.9.2 nompi_h135f659_114 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge libpng 1.6.43 h2797004_0 conda-forge libsanitizer 12.4.0 h46f95d5_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 12.4.0 ha4f9413_100 conda-forge libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.16 hd590300_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.12.7 h4c95cb1_3 conda-forge libzip 1.10.1 h2629f0a_3 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge markupsafe 2.1.5 py310h2372a71_0 conda-forge matplotlib-base 3.9.1 py310h0b1de36_0 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mistune 3.0.2 pyhd8ed1ab_0 conda-forge mmpbsa-py 16.0 pypi_0 pypi munkres 1.1.4 pyh9f0ad1d_0 conda-forge nbclient 0.10.0 pyhd8ed1ab_0 conda-forge nbconvert 7.16.4 hd8ed1ab_1 conda-forge nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge nbconvert-pandoc 7.16.4 hd8ed1ab_1 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncurses 6.5 h59595ed_0 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge netcdf-fortran 4.6.1 nompi_h228c76a_104 conda-forge notebook 7.2.1 pyhd8ed1ab_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge numpy 1.26.4 py310hb13e2d6_0 conda-forge ocl-icd 2.3.2 hd590300_1 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.3.1 h4bc722e_2 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge packmol 20.15.0 hc8b2c43_0 conda-forge packmol-memgen 2023.2.24 pypi_0 pypi pandas 2.2.2 py310hf9f9076_1 conda-forge pandoc 3.3 ha770c72_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge parmed 4.2.2 py310hc6cd4ac_1 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge pcre2 10.44 h0f59acf_0 conda-forge pdb-tools 2.5.0 pyhd8ed1ab_0 conda-forge pdb4amber 22.0 pypi_0 pypi perl 5.32.1 7_hd590300_perl5 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.4.0 py310hebfe307_0 conda-forge pip 24.1.2 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge plotly 5.23.0 pyhd8ed1ab_0 conda-forge pmx_biobb 4.1.3 py310he3a19b2_0 bioconda prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge prompt_toolkit 3.0.47 hd8ed1ab_0 conda-forge psutil 6.0.0 py310hc51659f_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge pycairo 1.26.1 py310he029307_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pymsmt 22.0 pypi_0 pypi pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.10.14 hd12c33a_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytraj 2.0.6 pypi_0 pypi pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge pyzmq 26.0.3 py310h6883aea_0 conda-forge qhull 2020.2 h434a139_5 conda-forge qtconsole-base 5.5.2 pyha770c72_0 conda-forge qtpy 2.4.1 pyhd8ed1ab_0 conda-forge rdkit 2023.03.3 py310h399bcf7_0 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.35.1 pyhd8ed1ab_0 conda-forge reportlab 4.2.2 py310hc51659f_0 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge rpds-py 0.19.1 py310h42e942d_0 conda-forge sander 22.0 pypi_0 pypi scipy 1.13.1 py310h93e2701_0 conda-forge send2trash 1.8.3 pyh0d859eb_0 conda-forge setuptools 71.0.4 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.2.1 ha2e4443_0 conda-forge sniffio 1.3.1 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge sqlalchemy 2.0.31 py310hc51659f_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge sysroot_linux-64 2.12 he073ed8_17 conda-forge tenacity 9.0.0 pyhd8ed1ab_0 conda-forge terminado 0.18.1 pyh0d859eb_0 conda-forge tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.4.1 py310hc51659f_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge typing-extensions 4.12.2 hd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge unicodedata2 15.1.0 py310h2372a71_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.2.2 pyhd8ed1ab_1 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 24.6.0 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 4.0.11 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 hb711507_1 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.5 h75354e8_4 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h4ab18f5_1 conda-forge zstandard 0.23.0 py310h64cae3c_0 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge ```
frannerin commented 3 months ago

Sorry my bad, one of the quote characters in the problematic .top file was wonky: instead of "